Biochem-chpt. 2

Enzyme key points (7)

- lower activation energy - increase the reaction rate - don't alter equilibrium constant - not changed or consumed - pH and temperature sensitive - don't affect overall /_\g - specific for particular reactions (enzyme specificity)

Hill's Coefficient (cooperativity)

- value indicates the nature of binding by the molecule - if > 1, positively cooperative binding is occuring (after 1 ligand is bound, the affinity of the enzyme for further ligands increases). - if < 1, negatively cooperative binding is occuring - if = 1, enzyme does not exhbit cooperative binding

Oxidoreductases (dehydrogenases)

-catalyze oxidation-reduction reactions - often have a cofactor - e- donor : reductant - e- acceptor: oxidant - enzymes usually have dehydrogenase or reductase in name

cofactors and coenzymes

-non protein, small molecules that can bind to the active site of an enzyme and participate in catalyzing the reaction (use ionization, protonation, deprotonation) -cofactors: usually inorganic molecules or metal ions -coenzymes: small organic groups such as vitamins or NAD, FAD, CoA

What are the 3 assumptions of the Micheals-Menten equation?

1. substrate concentration is constant during the reaction---> [E] <<<[S] 2. [ES] remains constant (rate of product formation is constant); reaction slows only when [S] is significantly depleted ---> [ES] to decrease. 3. reaction proceeds only forward. ALL assumptions are true only in the initial phase of the reaction.----> only the initial reaction rates are reported!

endonuclease

An enzyme that cleaves phosphodiester bonds within a DNA strand (NOT the end- exonuclease)

Acetylation of lysine residues in histones increases gene expression because: A. DNA is tightly bound to negatively charged amino acids on histones. B. the carboxyl oxygen atoms in acetyl groups form hydrogen bonds with nitrogenous bases. C. the salt bridges between charged amino acids and phosphate groups are disrupted. D. lysine residues in histones associate with positively charged phosphate groups in DNA. Incorrect

C; Histones associate with DNA by forming salt bridges between their positively charged residues and negatively charged phosphate groups on DNA. Acetylation of histones involves the transfer of an acetyl group to positively charged amino groups on lysine or arginine residues, increasing gene expression by disrupting salt bridges between histones and DNA.

Are cofactors or coenzymes ingested as dietary minerals?

Cofactors

Which reversible inhibition involves the occupancy of the active site? How can this inhibition be overcome? How are the Vmax and km affected?

Competitive inhibition; adding more substrate to increase substrate-to-inhibitor ratio; vmax is not affected (enzymes still react); km is higher (lower affinity).

What is the purpose of the Michaelis-Menten equation?

Describes how the rate of the reaction, v, depends on the concentration of E and S.

In the induced fit model, what kind of reaction is the binding of the substrate to an active site on an enzyme? The release?

Endergonic; exergonic

What are allosteric enzymes? What is the purpose of having allosteric sites? what binds here?

Enzymes with multiple binding sites. the active site, as well as allosteric sites; to regulate the availability of the active site; allosteric activators or inhibitors, which cause a conformational change in enzymes to make the active site more or less available.

Michaelis-Menten graph usually shows a ____ but can also show a _____ graph. why?

Hyperbola; sigmoidal S-shaped graph due to cooperativity among substrate binding sites.

Zymogen

Inactived form of an enzyme.

Michaelis constant

Km; substrate concentration at which reaction rate is 1/2Vmax (half of the enzyme's active sites are full). - higher km means lower affinity for substrates. Cannot be altered by changing E or S concentration.

The conversion of ATP to cyclic AMP and inorganic phosphate is most likely catalyzed by which class of enzymes?

Lyase, b/c they are responsible for the breakdown of a single molecule into 2 molecules without water of the transfer of e-.

Which reversible inhibition involves the ability to bind either to the enzyme or the enzyme-substrate complex with different affinity for each? where do they bind? What would it be called if it had the same affinity for both? How are the Vmax and km affected?

Mixed inhibition; allosteric site; noncompetitive inhibitor; -prefers binding enzyme- km increases (low affinity) - prefers binding ES complex- km decreases (increases affinity) - Vmax is always decreased with mixed inhibition

Which reversible inhibition involves binding to the allosteric site to induce a change in enzyme conformation? How are the Vmax and km affected?

Noncompetitive inhibition; vmax decreases (less enzyme available to react; km is not affected (enzymes that are still active maintain the affinity).

Classifications of enzymes (6- LI'L HOT)

Oxidoreductases Transferases Hydrolases Lyases Isomerases Ligases

catalytic efficiency (of enzyme)

Ratio of Kcat/Km; large Kcat (high turnover) and small km (high substrate affinity) => high catalytic efficiency => more efficient enzyme.

T or F: high salt concentration of the solution increases double helix stability while decreased salt concentration decreases stability.

T

T or F: longer DNA molecules take more time to both melt and reanneal.

T

What happens in a reaction as the amount of substrate increases?

The enzyme is able to increase its rate of reaction till it reaches a maximum enzymatic reaction rate (Vmax). At this point, adding more substrate will not do anything.

Which reversible inhibition involves binding only to the enzyme-substrate complex, preventing the release of the substrate in the active site? Where do these inhibitors bind? How are the Vmax and km affected? how does the graph look?

Uncompetitive inhibition; allosteric site; both decrease (formation of the ES complex creates a conformational change, allowing the inhibitor to bind allosterically). 2 parallel lines.

How can Kcat be calculated?**

Vmax / total enzyme concentration [E]

M-M Equation

Vo = Vmax[S] / Km+[S]

Particularly dangerous enzymes that must be tightly controlled are secreted as inactive _____.

Zymogens (most have the suffix -ogen). ex: digestive enzyme trypsin, if released in an uncontrolled manner, can digest the organ itself.

Michaelis-Menten equation When the reaction rate is equal to 1/2 Vmax, what is the Km equal to?

[S]

irreversible inhibition

active site is made unavailable for prolonged period of time or enzyme is permanently altered

Examples of transient modification

allosteric activation and inhibition

Ligases

catalyze addition or synthesis reactions, generally between large similar molecules, and often require ATP; small molecules are usually catalyzed by LYASES ( which don't usually require ATP).

Lyases

catalyze cleavage of a single molecule into 2 products don't require water as substrate. - can also act in reverse and synthesis the 2 molecules into one.

Hydrolases

catalyze cleavage with the addition of water; commonly named afer only substrate. ex: phosphatase, lipases, peptidases

What are the 4 types of reversible inhibition?

competitive, noncompetitive, mixed, uncompetitive

Lineweaver-Burk plots

double reciprocal graph of the Michaelis Menten equation yields a straight line x axis = -1/km *decreased if moves left* y axis = 1/vmax *decreased if moved up* useful when determining the type of INHIBITION that an enzyme is experiencing

Holoenzyme

enzyme with its cofactor

Covalently Modified Enzymes

enzymes can be activated or deactivated by phosphorylation or dephosphorylation (both could do either....must be experimentally tested). Can also be modified by covalent attachment of sugar groups (glycosylation); can tag an enzyme for transport in cell, or modify protein activity and selectivity.

Apoenzymes

enzymes without their cofactors

What are the 2 states that subunits and enzymes can exist in?

low-affinity tense state (T) High-affinity relaxed state (R) binding encourages transition from T to R state.

Cofactor

metal ions and minerals (m & ms)

Are enzymatic reactions restricted to a single cofactor or coenzyme?

no

cooperative binding

occurs when the binding of one ligand to a protein increases or decreases the affinity of that protein for another ligand; affinity changes result from CONFORMATIONAL CHANGES. Cooperative enzymes have multiple subunit and active sites.

Isomerases

rearrangement of the structure of molecules

What does Kcat measure?

the number of substrate molecules "turned over" or converted to product per enzyme molecule per second

Prosthetic groups

tightly bound cofactors or coenzymes that are necessary for enzyme function

Transferases

transfer functional groups - ex: kinases- Move phosphate groups (generally from ATP).